Senior Director / Vice President, Machine Learning (Generative Chemistry)

The role

You will lead AI/ML and cheminformatics projects to build multi-modal generative models for biomolecular design. You will manage a computational team and define AI strategies to drive drug discovery.

What you will do

• Lead development, implementation, control, and reporting of AI/ML or computational projects.
• Oversee method development, pipeline development, and LLM based agent/workflow design.
• Drive benchmarking, scaling, and implementation into production grade systems.
• Promote operational excellence in AI projects by educating cross-functional collaborators.
• Manage and coordinate internal scientists and engineers and cross functional project teams.
• Mentor early hires and support recruiting and interview.
• Contribute to project planning including budgets, resources, and timelines.
• Scout emerging literature and the AI/ML landscape to propose new development strategies.

Required qualifications

• MSc or PhD in Computer Science, AI/ML, Physics, Biophysics, or a related field
• 7+ years of experience scientific/engineering/computational in Pharma or Biotech settings
• Experience driving results through teams of engineers/scientists in dynamic, fast paced, entrepreneurial, and technical environments
• Evidence of sustained independent thought and creativity driving high impact across drug development and chemistry AI/ML projects
• Track record of leadership and contribution to decision making on progression of AI/ML models
• Python
• Modern ML frameworks (PyTorch or JAX/TensorFlow)
• Version control
• Databases
• Deep learning architectures
• Relevant informatics software
• Record of performance reflected in publications, patents, or high impact internal reports

Nice to have

• Industry AI/ML experience
• Breadth across domains such as protein modeling/design, cheminformatics/docking/ADMET, biophysics/MD, and LLM/agentic automation
• Strong presence in the ML community through publications and conference proceedings
• MLOps expertise: data contracts and lineage (e.g., DVC/LakeFS), experiment tracking (MLflow/W&B), secure AWS infrastructure (S3, Batch/ECS/EKS, SageMaker), Docker, IaC (Terraform/CDK), and CI/CD (GitH
• Generative modeling (diffusion/flow/VAEs) for sequences, graphs, or 3D structures; docking rescoring (e.g., gnina, DiffDock) and pose quality metrics
• Workflow orchestration (Airflow/Prefect/Argo), data warehouses (Redshift/Snowflake), vector search (FAISS/pgvector), and lightweight internal tools (FastAPI, Streamlit/Gradio)
• Familiarity with ML software development and cloud services (Docker, AWS Batch, Step Functions, EKS, AWS ParallelCluster, etc.)
• Experience with librariers like: rdkit, rosetta, prody, biopython, pymol, openmm, dagster, prefect, etc.
• Experience mentoring early hires, acting as interim Head of ML, and contributing to hiring plans and interview processes at startups

Benefits

• Healthcare coverage
• Annual incentive program
• Retirement benefits
• Broad range of other benefits

About the company

FL117 is a venture-back stealth AI x bio startup. Flagship Pioneering invents and builds platform companies to transform human health, sustainability and beyond.